Ancient mitogenomes of Lapita pigs confirm continuity of the Pacific Clade in Remote Oceania

Abstract

The movement of Lapita peoples into western Remote Oceania ∼ 3000 BP, and subsequent dispersal into Polynesia, is one of the most extensive migration events in human history. While the origins of these settlers and their commensal animals in the west are generally well understood, questions remain about their dispersal into eastern Remote Oceania, and post-settlement interactions. The pig, Sus scrofa, is one of the commensal animals carried across Remote Oceania, and previous genetic studies identified a single lineage, the “Pacific Clade”, linking Pacific pigs to Island and Peninsular Southeast Asia. Here, we present 16 complete mitogenomes (>99 % coverage) and 8 partial mitogenomes (>80 % coverage) from eleven Remote Oceanic archaeological sites, spanning the Lapita period to the historic period. Phylogenetic analyses show a continuous pig population in Remote Oceania from their first introduction ∼ 3000 BP. Furthermore, sustained pig mitochondrial diversity is detected in western Remote Oceania from the Lapita period until today. In comparison, very limited diversity is found in eastern Remote Oceania, suggesting a bottleneck associated with human expansion into East Polynesia. The contrasting genetic signatures between west and east suggest that little to no pig movement occurred between these regions following the initial settlement of Polynesia. Comparison of the newly generated sequences to previously published ancient pig mitogenomes reveals the first ancient Pacific Clade pig in China, extending their range geographically to mainland East Asia, and temporally to 7000–6000 BP. Overall, this study contributes to a more nuanced understanding of Remote Oceania's settlement and pig husbandry.